Re: colvars error running ABF

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 13 2010 - 22:03:23 CDT

On Tue, Apr 13, 2010 at 9:47 PM, Patrick Yee <pyee_at_nd.edu> wrote:
> Hi NAMD users,
>
> After upgrading to NAMD 2.7b2 with the colvars module, I've found a
> problem in running ABF simulations. I get that there is a "FATAL
> ERROR: Input/Output error." Note that lines 12, 14, and 15 mention

I/O errors come from the file system not the application.
you could be running out of disk quota, have a broken disk,
or have a failing NFS, AFS, or other network FS.

i would check that. type: dmesg
on the compute node and check for suspicious messages
from the kernel.

cheers,
    axel.

> TCL. Does anyone have any idea how to remove this problem? The full
> message is:
>
> FATAL ERROR: Input/output error
> [0] Stack Traceback:
> [0] CmiAbort+0x7f  [0xab6a31]
> [1] _Z8NAMD_diePKc+0x62  [0x5093f2]
> [2] _Z13write_dcdstepiiPfS_S_Pd+0x650  [0x50a494]
> [3] _ZN6Output14output_dcdfileEiiP11FloatVectorPK7Lattice+0x4a8  [0x91891e]
> [4] _ZN6Output10coordinateEiiP6VectorP11FloatVectorR7Lattice+0x9b  [0x916a05]
> [5] _ZN24CkIndex_CollectionMaster39_call_receivePositions_CollectVectorMsgEPvP16CollectionMaster+0x18f
>  [0x51bfc3]
> [6] CkDeliverMessageFree+0x21  [0xa343cb]
> [7] _Z15_processHandlerPvP11CkCoreState+0x59a  [0xa33a26]
> [8] CsdScheduleForever+0xa5  [0xabd4b9]
> [9] CsdScheduler+0x1c  [0xabd0ba]
> [10] _ZN7BackEnd7suspendEv+0xb  [0x511f6d]
> [11] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x140  [0x971f6c]
> [12] TclInvokeStringCommand+0x91  [0xae11d8]
> [13] /afs/crc.nd.edu/x86_64_linux/namd/NAMD_2.7b2_Linux-x86_64/namd2 [0xb17028]
> [14] Tcl_EvalEx+0x176  [0xb1766b]
> [15] Tcl_EvalFile+0x134  [0xb0f074]
> [16] _ZN9ScriptTcl3runEPc+0x14  [0x97166a]
> [17] _Z18after_backend_initiPPc+0x22b  [0x50dc0b]
> [18] main+0x3a  [0x50d9aa]
> [19] __libc_start_main+0xf4  [0x36d461d994]
> [20] _ZNSt8ios_base4InitD1Ev+0x52  [0x508d5a]
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:53 CST